SMTL ID : 1f74.1

CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II COMPLEXED WITH 4-DEOXY-SIALIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x NAY: 6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-2-OXONONANOIC ACID(Non-covalent)

NAY.1: 16 residues within 4Å: Chain A: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.246, L.250 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.10 Hydrogen bonds: A:S.47, A:T.48, A:T.48, A:Y.136, A:G.188, A:D.190, A:D.190, A:S.207, A:S.207 Water bridges: A:S.47, A:T.48, A:K.164, C:Y.110 Salt bridges: A:K.164 NAY.5: 16 residues within 4Å: Chain B: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.246, L.250 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.10 Hydrogen bonds: B:S.47, B:T.48, B:Y.136, B:Y.136, B:G.188, B:D.190, B:D.190, B:S.207, B:S.207 Water bridges: B:S.47, B:T.48, B:K.164, B:K.164 Salt bridges: B:K.164 NAY.8: 16 residues within 4Å: Chain C: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.246, L.250 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.10 Hydrogen bonds: C:S.47, C:T.48, C:T.48, C:Y.136, C:G.188, C:D.190, C:D.190, C:S.207, C:S.207 Water bridges: C:S.47, C:T.48, C:K.164, A:Y.110 Salt bridges: C:K.164 NAY.12: 16 residues within 4Å: Chain D: A.10, Y.43, G.46, S.47, T.48, Y.136, K.164, G.188, F.189, D.190, E.191, I.205, G.206, S.207, L.246, L.250 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.10 Hydrogen bonds: D:S.47, D:T.48, D:Y.136, D:Y.136, D:G.188, D:D.190, D:D.190, D:S.207, D:S.207 Water bridges: D:S.47, D:T.48, D:K.164, D:K.164 Salt bridges: D:K.164

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.2, K.67, D.72, G.99, D.101 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.2, A:K.67, A:K.67, A:D.101 Water bridges: A:R.2, A:K.67 GOL.3: 5 residues within 4Å: Chain A: G.226, K.227, L.228, K.229, E.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.228, A:K.229, A:E.230, A:E.230, A:E.230 GOL.6: 4 residues within 4Å: Chain B: Q.218, L.222, E.230 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.230 GOL.7: 3 residues within 4Å: Chain B: V.214, Q.218 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.218 Water bridges: B:Q.218 GOL.9: 5 residues within 4Å: Chain C: R.2, K.67, D.72, G.99, D.101 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.2, C:K.67, C:K.67, C:D.101 Water bridges: C:R.2, C:K.67 GOL.10: 5 residues within 4Å: Chain C: G.226, K.227, L.228, K.229, E.230 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.228, C:K.229, C:E.230, C:E.230, C:E.230 GOL.13: 4 residues within 4Å: Chain D: Q.218, L.222, E.230 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.230 GOL.14: 3 residues within 4Å: Chain D: V.214, Q.218 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.218 Water bridges: D:Q.218

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain B: Y.180, P.181, N.182, H.183 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain D: Y.180, P.181, N.182, H.183 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barbosa, J.A.R.G. et al., Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme. J.Mol.Biol. (2000)

Release Date

2000-11-22

Peptides

N-ACETYL-NEURAMINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

N-ACETYL-NEURAMINATE LYASE

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